Hi! Author here. You're right — but two things to consider here.
First, that quote is referring to human-made systems, not natural ones (as is the rest of the essay!) and I think our views align on whether human systems regularly work.
Second, natural systems (and all complex-enough systems) are always running in some degraded fashion. So what "working" means is ambiguous: they are broken, yet accomplishing the goal. The quote from the essay refers to "working" in the "free of faults" sense, in which I again think our views align.